Integration and representation of heterogeneous metabolic databases for the analysis of metabolism: BIOSILICO
Jin Sik Kim1, Ji Hoon Jun2, Yong Wook Kim, Sujin Chae, Mira Roh, Yong-Ho In and Sang Yup Lee
1jskim@mail.kaist.ac.kr, KAIST; 2gene2@bioinfomatix.com, Bioinfomatix Inc.
As the number of completely sequenced genomes increases, more and more biological data generated from the analysis of the genomes are becoming available. Through the annotation and molecular analysis of these sequenced genomes, numerous genes that encode enzymes catalyzing various metabolic reactions have been identified. Quantitative as well as qualitative analyses of metabolic pathways involving various metabolic reactions are important for the elucidation of the metabolic and physiological characteristics of organisms. BIOSILICO is a web-based database system that facilitates the search and analysis of metabolic pathways. BIOSILICO allows efficient retrieval of all available information on enzymes, biochemical compounds and biological reactions and pathways by integrating the heterogeneous metabolic databases including LIGAND, ENZYME, EcoCyc and MetaCyc, and generates well-designed view pages showing retrieved data in a systematic way for easy understanding. The system is installed on the IBM system running IBM AIX 4.3 operating system. BIOSILICO uses the IBM DB2 UDB and the MySQL as DBMS. BIOSILICO is developed as an extensible system with a robust systematic architecture.
(This work was supported by the Advanced Backbone IT Technology Development Project (IMT2000-C3-1) of the Ministry of Information and Communication (MIC) and Korean Ministry of Science and Technology (MOST) and by the National Research Laboratory Program of the MOST. Hardware support by the IBM-SUR program is greatly appreciated.)